Different scenarios and their prioritization were identified for the Sacca di Goro (Adriatic Sea, Northern Italy), an eutrophic lagoon which is exploited with extensive clam farming activities. A preliminary scenario assessment was investigated with qualitative modelling. Economic and environmental variables were accommodated in a comprehensive model of the lagoon that describes major interactions between selected compartments. This kind of analysis is specially suited for systems that are partially specified. In a second step, we addressed the first priority scenario identified by end-users and which concerns clam farming activities in the lagoon. This scenario was analysed using a quantitative approach based on a 3D integrated hydrodynamic-biogeochemical model. Such approach allowed the assessment of the implications of an increase in the clam farming area. The first results seems to indicate that a further increase of clam farming areas (or a more intense exploitation) inside the Sacca di Goro lagoon would increase the risk of anoxia and the vulnerability of clam farming to Ulva blooms. On the contrary, an increase in the exploitation area outside the lagoon will increase the average productivity and maintain constant the risks of anoxia and the vulnerability to Ulva blooms. Furthermore, the cost of measures taken by the local and regional authorities for the lagoon management and to control nuisance macroalgal blooms are potentially compensated by the increase in clams production predicted by the model. The focus on clam farming provides only a partial view of a more complex system which composes by agriculture, urban, touristic areas, and natural sites and is under the influence of climate changes. However, such scenarios constitute only the first stage in the procedure of overall lagoon scenario analysis, and a second iteration is necessary to define the main constraints and boundaries, as well as to incorporate the economic evaluation and social implications of the different options.